Publications by authors named "Satish Singh"

147 Publications

Interaction of zinc oxide nanoparticles with soil: Insights into the chemical and biological properties.

Environ Geochem Health 2021 Apr 17. Epub 2021 Apr 17.

Southern Federal University, Rostov-on-Don, Russia, 344090.

Widespread use of zinc oxide nanoparticles (ZnO-NPs) threatens soil, plants, terrestrial and aquatic animals. Thus, it is essential to explore the fate and behavior of NPs in soil and also its mechanism of interaction with soil microbial biodiversity to maintain soil health and quality to accomplish essential ecosystem services. With this background, the model experiment was conducted in the greenhouse to study the impact of ZnO-NPs on soil taking maize as a test crop. The X-ray diffraction, Fourier transform infrared spectroscopy, Scanning electron microscopy and Particles size analysis of engineered NPs confirmed that the material was ZnO-NPs (particle size--65.82 nm). The application of ZnO-NPs resulted in a significant decrease in soil pH. Significantly high EC (0.13 dS m) was recorded where ZnO-NPs were applied at the rate of 2.5 mg Zn kg soil over control (0.12 dS m). A significant increase in soil available phosphorus was observed on applying ZnO-NPs (15.29 mg kg of soil) as compared to control (11.84 mg kg of soil). Maximum soil available Zn (2.09 mg kg) was recorded in ZnO-NPs-amended soil (T) which was significantly higher than control (0.33 mg kg) as well as treatments containing conventional zincatic fertilizers. The inhibition rates of dehydrogenase enzyme activity in the presence of 0.5 mg, 1.25 mg and 2.5 mg ZnO-NPs per kg soil were 31.3, 46.2 and 49.7%, respectively. Soil microbial biomass carbon was significantly reduced (103.33 µg g soil) in soils treated with ZnO-NPs over control (111.33 µg g soil). Soil bacterial count was also significantly lesser (12.33 × 10 CFU) in the case where 2.5 mg kg ZnO-NPs were applied as compared to control (21.33 × 10 CFU). The corresponding decrease in fungal and actinomycetes colony count was 24.16, 37.35, 46.15% and 14.59, 17.97, 22.45% with the application of 0.5 mg, 1.25 mg and 2.5 mg ZnO-NPs per kg soil, respectively, as compared to control. Thus, the use of ZnO-NPs resulted in an increase in soil available Zn but inhibited soil microbial activity.
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http://dx.doi.org/10.1007/s10653-021-00929-8DOI Listing
April 2021

Semibrittle seismic deformation in high-temperature mantle mylonite shear zone along the Romanche transform fault.

Sci Adv 2021 Apr 9;7(15). Epub 2021 Apr 9.

Università di Modena e Reggio Emilia, Modena, Italy.

Oceanic transform faults, a key element of plate tectonics, represent the first-order discontinuities along mid-ocean ridges, host large earthquakes, and induce extreme thermal gradients in lithosphere. However, the thermal structure along transform faults and its effects on earthquake generation are poorly understood. Here we report the presence of a 10- to 15-kilometer-thick in-depth band of microseismicity in 10 to 34 kilometer depth range associated with a high-temperature (700° to 900°C) mantle below the brittle lithosphere along the Romanche mega transform fault in the equatorial Atlantic Ocean. The occurrence of the shallow 2016 moment magnitude 7.1 supershear rupture earthquake and these deep microearthquakes indicate that although large earthquakes occur in the upper brittle lithosphere, a substantial amount of deformation is accommodated in the semibrittle mylonitic mantle that resides at depths below the 600°C isotherm. We also observe a rapid westward deepening of this band of seismicity indicating a strong lateral heterogeneity.
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http://dx.doi.org/10.1126/sciadv.abf3388DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8034845PMC
April 2021

Artificial Intelligence-Based Assessment of Colorectal Polyp Histology by Elastic-Scattering Spectroscopy.

Dig Dis Sci 2021 Mar 24. Epub 2021 Mar 24.

Research Service, VA Boston Healthcare System, 150 South Huntington Ave., Boston, MA, 02130, USA.

Background: Colonoscopic screening and surveillance for colorectal cancer could be made safer and more efficient if endoscopists could predict histology without the need to biopsy and perform histopathology on every polyp. Elastic-scattering spectroscopy (ESS), using fiberoptic probes integrated into standard biopsy tools, can assess, both in vivo and in real time, the scattering and absorption properties of tissue related to its underlying pathology.

Aims: The objective of this study was to evaluate prospectively the potential of ESS to predict polyp pathology accurately.

Methods: We obtained ESS measurements from patients undergoing screening/surveillance colonoscopy using an ESS fiberoptic probe integrated into biopsy forceps. The integrated forceps were used for tissue acquisition, following current standards of care, and optical measurement. All measurements were correlated to the index pathology. A machine learning model was then applied to measurements from 367 polyps in 169 patients to prospectively evaluate its predictive performance.

Results: The model achieved sensitivity of 0.92, specificity of 0.87, negative predictive value (NPV) of 0.87, and high-confidence rate (HCR) of 0.84 for distinguishing 220 neoplastic polyps from 147 non-neoplastic polyps of all sizes. Among 138 neoplastic and 131 non-neoplastic polyps ≤ 5 mm, the model achieved sensitivity of 0.91, specificity of 0.88, NPV of 0.89, and HCR of 0.83.

Conclusions: Results show that ESS is a viable endoscopic platform for real-time polyp histology, particularly for polyps ≤ 5 mm. ESS is a simple, low-cost, clinically friendly, optical biopsy modality that, when interfaced with minimally obtrusive endoscopic tools, offers an attractive platform for in situ polyp assessment.
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http://dx.doi.org/10.1007/s10620-021-06901-xDOI Listing
March 2021

Alpha2-Antiplasmin: The Devil You Don't Know in Cerebrovascular and Cardiovascular Disease.

Front Cardiovasc Med 2020 23;7:608899. Epub 2020 Dec 23.

Department of Medicine, University of Arizona-College of Medicine, Phoenix, AZ, United States.

Alpha2-antiplasmin (α2AP), the fast-reacting, serine protease inhibitor (serpin) of plasmin, was originally thought to play a key role in protection against uncontrolled, plasmin-mediated proteolysis of coagulation factors and other molecules. However, studies of humans and mice with genetic deficiency of α2AP have expanded our understanding of this serpin, particularly in disease states. Epidemiology studies have shown an association between high α2AP levels and increased risk or poor outcome in cardiovascular diseases. Mechanistic studies in disease models indicate that α2AP stops the body's own fibrinolytic system from dissolving pathologic thrombi that cause venous thrombosis, pulmonary embolism, arterial thrombosis, and ischemic stroke. In addition, α2AP fosters the development of microvascular thrombosis and enhances matrix metalloproteinase-9 expression. Through these mechanisms and others, α2AP contributes to brain injury, hemorrhage and swelling in experimental ischemic stroke. Recent studies also show that α2AP is required for the development of stasis thrombosis by inhibiting the early activation of effective fibrinolysis. In this review, we will discuss the key role played by α2AP in controlling thrombosis and fibrinolysis and, we will consider its potential value as a therapeutic target in cardiovascular diseases and ischemic stroke.
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http://dx.doi.org/10.3389/fcvm.2020.608899DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7785519PMC
December 2020

An end-to-end breast tumour classification model using context-based patch modelling - A BiLSTM approach for image classification.

Comput Med Imaging Graph 2021 Jan 4;87:101838. Epub 2020 Dec 4.

School of Computing, National University of Singapore, 13 Computing Drive, 117417 Singapore, Singapore; Bioinformatics Institute, A*STAR, 30 Biopolis Street, 138671 Singapore, Singapore; Image and Pervasive Access Lab (IPAL), CNRS UMI 2955, 1 Fusionopolis Way, 138632 Singapore, Singapore; Singapore Eye Research Institute, 20 College Road, 169856 Singapore, Singapore.

Researchers working on computational analysis of Whole Slide Images (WSIs) in histopathology have primarily resorted to patch-based modelling due to large resolution of each WSI. The large resolution makes WSIs infeasible to be fed directly into the machine learning models due to computational constraints. However, due to patch-based analysis, most of the current methods fail to exploit the underlying spatial relationship among the patches. In our work, we have tried to integrate this relationship along with feature-based correlation among the extracted patches from the particular tumorous region. The tumour regions extracted from WSI have arbitrary dimensions having the range 20,570 to 195 pixels across width and 17,290 to 226 pixels across height. For the given task of classification, we have used BiLSTMs to model both forward and backward contextual relationship. Also, using RNN based model, the limitation of sequence size is eliminated which allows the modelling of variable size images within a deep learning model. We have also incorporated the effect of spatial continuity by exploring different scanning techniques used to sample patches. To establish the efficiency of our approach, we trained and tested our model on two datasets, microscopy images and WSI tumour regions. Both datasets were published by ICIAR BACH Challenge 2018. Finally, we compared our results with top 5 teams who participated in the BACH challenge and achieved the top accuracy of 90% for microscopy image dataset. For WSI tumour region dataset, we compared the classification results with state of the art deep learning networks such as ResNet, DenseNet, and InceptionV3 using maximum voting technique. We achieved the highest performance accuracy of 84%. We found out that BiLSTMs with CNN features have performed much better in modelling patches into an end-to-end Image classification network. Additionally, the variable dimensions of WSI tumour regions were used for classification without the need for resizing. This suggests that our method is independent of tumour image size and can process large dimensional images without losing the resolution details.
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http://dx.doi.org/10.1016/j.compmedimag.2020.101838DOI Listing
January 2021

Seismic Crustal Structure and Morphotectonic Features Associated With the Chain Fracture Zone and Their Role in the Evolution of the Equatorial Atlantic Region.

J Geophys Res Solid Earth 2020 Oct 23;125(10):e2020JB020275. Epub 2020 Sep 23.

GEOMAR Helmholtz Centre of Ocean Research Kiel, RD4-Marine Geodynamics Kiel Germany.

Oceanic transform faults and fracture zones (FZs) represent major bathymetric features that keep the records of past and present strike-slip motion along conservative plate boundaries. Although they play an important role in ridge segmentation and evolution of the lithosphere, their structural characteristics, and their variation in space and time, are poorly understood. To address some of the unknowns, we conducted interdisciplinary geophysical studies in the equatorial Atlantic Ocean, the region where some of the most prominent transform discontinuities have been developing. Here we present the results of the data analysis in the vicinity of the Chain FZ, on the South American Plate. The crustal structure across the Chain FZ, at the contact between ∼10 and 24 Ma oceanic lithosphere, is sampled along seismic reflection and refraction profiles. We observe that the crustal thickness within and across the Chain FZ ranges from ∼4.6-5.9 km, which compares with the observations reported for slow-slipping transform discontinuities globally. We attribute this presence of close to normal oceanic crustal thickness within FZs to the mechanism of lateral dike propagation, previously considered to be valid only in fast-slipping environments. Furthermore, the combination of our results with other data sets enabled us to extend the observations to morphotectonic characteristics on a regional scale. Our broader view suggests that the formation of the transverse ridge is closely associated with a global plate reorientation that was also responsible for the propagation and for shaping lower-order Mid-Atlantic Ridge segmentation around the equator.
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http://dx.doi.org/10.1029/2020JB020275DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7685155PMC
October 2020

Advanced endoscopic imaging for detecting and guiding therapy of early neoplasias of the esophagus.

Ann N Y Acad Sci 2020 12 12;1482(1):61-76. Epub 2020 Nov 12.

VA Boston Healthcare System, Boston, Massachusetts.

Esophageal cancers, largely adenocarcinoma in Western countries and squamous cell cancer in Asia, present a significant burden of disease and remain one of the most lethal of cancers. Key to improving survival is the development and adoption of new imaging modalities to identify early neoplastic lesions, which may be small, multifocal, subsurface, and difficult to detect by standard endoscopy. Such advanced imaging is particularly relevant with the emergence of ablative techniques that often require multiple endoscopic sessions and may be complicated by bleeding, pain, strictures, and recurrences. Assessing the specific location, depth of involvement, and features correlated with neoplastic progression or incomplete treatment may optimize treatments. While not comprehensive of all endoscopic imaging modalities, we review here some of the recent advances in endoscopic luminal imaging, particularly with surface contrast enhancement using virtual chromoendoscopy, highly magnified subsurface imaging with confocal endomicroscopy, optical coherence tomography, elastic scattering spectroscopy, angle-resolved low-coherence interferometry, and light scattering spectroscopy. While there is no single ideal imaging modality, various multimodal instruments are also being investigated. The future of combining computer-aided assessments, molecular markers, and improved imaging technologies to help localize and ablate early neoplastic lesions shed hope for improved disease outcome.
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http://dx.doi.org/10.1111/nyas.14523DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7780427PMC
December 2020

Real-time artificial intelligence-based histologic classification of colorectal polyps with augmented visualization.

Gastrointest Endosc 2021 03 16;93(3):662-670. Epub 2020 Sep 16.

Research Service, VA Boston Healthcare System, Boston, MA; Department of Biomedical Engineering, Boston University College of Engineering, Boston, MA; Department of Medicine, Section of Gastroenterology, VA Boston Healthcare System, Boston, MA; Department of Medicine, Boston University School of Medicine, Boston, MA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA.

Background And Aims: Artificial intelligence (AI)-based computer-aided diagnostic (CADx) algorithms are a promising approach for real-time histology (RTH) of colonic polyps. Our aim is to present a novel in situ CADx approach that seeks to increase transparency and interpretability of results by generating an intuitive augmented visualization of the model's predicted histology over the polyp surface.

Methods: We developed a deep learning model using semantic segmentation to delineate polyp boundaries and a deep learning model to classify subregions within the segmented polyp. These subregions were classified independently and were subsequently aggregated to generate a histology map of the polyp's surface. We used 740 high-magnification narrow-band images from 607 polyps in 286 patients and over 65,000 subregions to train and validate the model.

Results: The model achieved a sensitivity of .96, specificity of .84, negative predictive value (NPV) of .91, and high-confidence rate (HCR) of .88, distinguishing 171 neoplastic polyps from 83 non-neoplastic polyps of all sizes. Among 93 neoplastic and 75 non-neoplastic polyps ≤5 mm, the model achieved a sensitivity of .95, specificity of .84, NPV of .91, and HCR of .86.

Conclusions: The CADx model is capable of accurately distinguishing neoplastic from non-neoplastic polyps and provides a histology map of the spatial distribution of localized histologic predictions along the delineated polyp surface. This capability may improve interpretability and transparency of AI-based RTH and offer intuitive, accurate, and user-friendly guidance in real time for the clinical management and documentation of optical histology results.
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http://dx.doi.org/10.1016/j.gie.2020.09.018DOI Listing
March 2021

Discovery of flat seismic reflections in the mantle beneath the young Juan de Fuca Plate.

Nat Commun 2020 Aug 17;11(1):4122. Epub 2020 Aug 17.

Lamont-Doherty Earth Observatory, Columbia University, 61 Route 9W, Palisades, NY, 10964-1000, USA.

Crustal properties of young oceanic lithosphere have been examined extensively, but the nature of the mantle lithosphere underneath remains elusive. Using a novel wide-angle seismic imaging technique, here we show the presence of two sub-horizontal reflections at ∼11 and ∼14.5 km below the seafloor over the 0.51-2.67 Ma old Juan de Fuca Plate. We find that the observed reflectors originate from 300-600-m-thick layers, with an ∼7-8% drop in P-wave velocity. They could be explained either by the presence of partially molten sills or frozen gabbroic sills. If partially molten, the shallower sill would define the base of a thin lithosphere with the constant thickness (11 km), requiring the presence of a mantle thermal anomaly extending up to 2.67 Ma. In contrast, if these reflections were frozen melt sills, they would imply the presence of thick young oceanic lithosphere (20-25 km), and extremely heterogeneous upper mantle.
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http://dx.doi.org/10.1038/s41467-020-17946-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7431579PMC
August 2020

Ibrutinib Resistance Mechanisms and Treatment Strategies for B-Cell lymphomas.

Cancers (Basel) 2020 May 22;12(5). Epub 2020 May 22.

Department of Medical Oncology & Hematology, All India Institute of Medical Sciences, Rishikesh 249203, India.

Chronic activation of B-cell receptor (BCR) signaling via Bruton tyrosine kinase (BTK) is largely considered to be one of the primary mechanisms driving disease progression in B-Cell lymphomas. Although the BTK-targeting agent ibrutinib has shown promising clinical responses, the presence of primary or acquired resistance is common and often leads to dismal clinical outcomes. Resistance to ibrutinib therapy can be mediated through genetic mutations, up-regulation of alternative survival pathways, or other unknown factors that are not targeted by ibrutinib therapy. Understanding the key determinants, including tumor heterogeneity and rewiring of the molecular networks during disease progression and therapy, will assist exploration of alternative therapeutic strategies. Towards the goal of overcoming ibrutinib resistance, multiple alternative therapeutic agents, including second- and third-generation BTK inhibitors and immunomodulatory drugs, have been discovered and tested in both pre-clinical and clinical settings. Although these agents have shown high response rates alone or in combination with ibrutinib in ibrutinib-treated relapsed/refractory(R/R) lymphoma patients, overall clinical outcomes have not been satisfactory due to drug-associated toxicities and incomplete remission. In this review, we discuss the mechanisms of ibrutinib resistance development in B-cell lymphoma including complexities associated with genomic alterations, non-genetic acquired resistance, cancer stem cells, and the tumor microenvironment. Furthermore, we focus our discussion on more comprehensive views of recent developments in therapeutic strategies to overcome ibrutinib resistance, including novel BTK inhibitors, clinical therapeutic agents, proteolysis-targeting chimeras and immunotherapy regimens.
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http://dx.doi.org/10.3390/cancers12051328DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7281539PMC
May 2020

Integration of VEK-30 peptide enhances fibrinolytic properties of staphylokinase.

Biotechnol Appl Biochem 2021 Apr 20;68(2):213-220. Epub 2020 May 20.

CSIR-Institute of Microbial Technology, Chandigarh, India.

Staphylokinase (SAK), a 136 amino acid bacterial protein with profibrinolytic properties, has emerged as an important thrombolytic agent because of its fibrin specificity and reduced inhibition by α-2 antiplasmin. In an attempt to enhance the clot dissolution ability of SAK, a 30 amino acid peptide (VEK-30) derived from a plasminogen (Pg) binding protein (PAM), was fused at the C-terminal end of SAK with a RGD (Arg-Gly-Asp) linker. The chimeric protein, SAKVEK, was expressed in E. coli and purified as a soluble protein. Pg activation by equimolar complexes of SAKVEK and SAK with plasmin revealed that the fusion of VEK-30 peptide has significantly enhanced the catalytic activity of SAK. The kinetic constant, k /K , of SAKVEK for the substrate Pg appeared 2.7 times higher than that of SAK and the time required for the fibrin and platelet rich clot lysis was shortened by 30% and 50%, respectively. The binary activator complex of SAKVEK with plasmin gets inhibited by α2- antiplasmin but remains protected in the presence of fibrin, very similar to SAK. Thus, the present study suggests that SAKVEK is more potent and effective as a thrombolytic agent due to its higher catalytic activity for Pg activation in a fibrin-specific manner and its ability to clear platelet-rich plasma clot faster than SAK.
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http://dx.doi.org/10.1002/bab.1912DOI Listing
April 2021

Correction to: In Vivo Stability of Therapeutic Proteins.

Pharm Res 2020 03 12;37(3):68. Epub 2020 Mar 12.

Drug Product Services, Lonza AG, Basel, Switzerland.

A manuscript version without peer-review revisions was mistakenly processed and published.
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http://dx.doi.org/10.1007/s11095-020-2780-7DOI Listing
March 2020

A Semi-Physical Platform for Guidance and Formations of Fixed-Wing Unmanned Aerial Vehicles.

Sensors (Basel) 2020 Feb 19;20(4). Epub 2020 Feb 19.

Delft Center for Systems and Control, Delft University of Technology, 2626CD Delft, The Netherlands.

Unmanned Aerial Vehicles (UAVs) have multi-domain applications, fixed-wing UAVs being a widely used class. Despite the ongoing research on the topics of guidance and formation control of fixed-wing UAVs, little progress is known on implementation of semi-physical validation platforms (software-in-the-loop or hardware-in-the-loop) for such complex autonomous systems. A semi-physical simulation platform should capture not only the physical aspects of UAV dynamics, but also the cybernetics aspects such as the autopilot and the communication layers connecting the different components. Such a cyber-physical integration would allow validation of guidance and formation control algorithms in the presence of uncertainties, unmodelled dynamics, low-level control loops, communication protocols and unreliable communication: These aspects are often neglected in the design of guidance and formation control laws for fixed-wing UAVs. This paper describes the development of a semi-physical platform for multi-fixed wing UAVs where all the aforementioned points are carefully integrated. The environment adopts Raspberry Pi's programmed in C++, which can be interfaced to standard autopilots (PX4) as a companion computer. Simulations are done in a distributed setting with a server program designed for the purpose of routing data between nodes, handling the user inputs and configurations of the UAVs. Gazebo-ROS is used as a 3D visualization tool.
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http://dx.doi.org/10.3390/s20041136DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7070914PMC
February 2020

In Vivo Stability of Therapeutic Proteins.

Pharm Res 2020 Jan 3;37(2):23. Epub 2020 Jan 3.

Lonza AG, Drug Product Services, Basel, Switzerland.

Significant efforts are made to characterize molecular liabilities and degradation of the drug substance (DS) and drug product (DP) during various product life-cycle stages. The in vivo fate of a therapeutic protein is usually only considered in terms of pharmacokinetics (PKs) and pharmacodynamics (PDs). However, the environment in the human body differs substantially from that of the matrix (formulation) of the DP and may impact on the stability of an injected therapeutic protein. Stabilizing excipients used in protein formulations are expected to undergo more rapid distribution and dissociation in vivo, compared to a protein as a highly charged macromolecule. Thus, in vivo stability may significantly differ from shelf-life stability. In vivo degradation of the therapeutic protein may alter efficacy and/or safety characteristics such as immunogenicity. Studying the stability of a therapeutic protein in the intended body compartment can de-risk drug development in early stages of development by improving the selection of better clinical lead molecules. This review assesses the considerations when aiming to evaluate the in vivo fate of a therapeutic protein by comparing the physiology of relevant human body compartments and assessing their potential implications on the stability of a therapeutic protein. Moreover, we discuss the limitations of current experimental approaches mimicking physiologic conditions, depending on the desired route of administration, such as intravenous (IV), subcutaneous (SC), intravitreal (IVT), or intrathecal (IT) administration(s). New models more closely mimicking the relevant physiologic environment and updated analytical methods are required to understand the in vivo fate of therapeutic proteins.
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http://dx.doi.org/10.1007/s11095-019-2689-1DOI Listing
January 2020

diffGrad: An Optimization Method for Convolutional Neural Networks.

IEEE Trans Neural Netw Learn Syst 2020 11 29;31(11):4500-4511. Epub 2020 Oct 29.

Stochastic gradient descent (SGD) is one of the core techniques behind the success of deep neural networks. The gradient provides information on the direction in which a function has the steepest rate of change. The main problem with basic SGD is to change by equal-sized steps for all parameters, irrespective of the gradient behavior. Hence, an efficient way of deep network optimization is to have adaptive step sizes for each parameter. Recently, several attempts have been made to improve gradient descent methods such as AdaGrad, AdaDelta, RMSProp, and adaptive moment estimation (Adam). These methods rely on the square roots of exponential moving averages of squared past gradients. Thus, these methods do not take advantage of local change in gradients. In this article, a novel optimizer is proposed based on the difference between the present and the immediate past gradient (i.e., diffGrad). In the proposed diffGrad optimization technique, the step size is adjusted for each parameter in such a way that it should have a larger step size for faster gradient changing parameters and a lower step size for lower gradient changing parameters. The convergence analysis is done using the regret bound approach of the online learning framework. In this article, thorough analysis is made over three synthetic complex nonconvex functions. The image categorization experiments are also conducted over the CIFAR10 and CIFAR100 data sets to observe the performance of diffGrad with respect to the state-of-the-art optimizers such as SGDM, AdaGrad, AdaDelta, RMSProp, AMSGrad, and Adam. The residual unit (ResNet)-based convolutional neural network (CNN) architecture is used in the experiments. The experiments show that diffGrad outperforms other optimizers. Also, we show that diffGrad performs uniformly well for training CNN using different activation functions. The source code is made publicly available at https://github.com/shivram1987/diffGrad.
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http://dx.doi.org/10.1109/TNNLS.2019.2955777DOI Listing
November 2020

Freezing of Biologicals Revisited: Scale, Stability, Excipients, and Degradation Stresses.

J Pharm Sci 2020 01 6;109(1):44-61. Epub 2019 Nov 6.

Pharmaceutical Development, Allergan Inc., Irvine, California 92612. Electronic address:

Although many biotech products are successfully stored in the frozen state, there are cases of degradation of biologicals during freeze storage. These examples are discussed in the Perspective to emphasize the fact that stability of frozen biologicals should not be taken for granted. Frozen-state degradation (predominantly, aggregation) has been linked to crystallization of a cryoprotector in many cases. Other factors, for example, protein unfolding (either due to cold denaturation or interaction of protein molecules with ice crystals), could also contribute to the instability. As a hypothesis, additional freezing-related destabilization pathways are introduced in the paper, that is, air bubbles formed on the ice crystallization front, and local pressure and mechanical stresses due to volume expansion during water-to-ice transformation. Furthermore, stability of frozen biologicals can depend on the sample size, via its impact on the freezing kinetics (i.e., cooling rates and freezing time) and cryoconcentration effects, as well as on the mechanical stresses associated with freezing. We conclude that, although fundamentals of freezing processes are fairly well described in the current literature, there are important gaps to be addressed in both scientific foundations of the freezing-related manufacturing processes and implementation of the available knowledge in practice.
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http://dx.doi.org/10.1016/j.xphs.2019.10.062DOI Listing
January 2020

Computer-assisted assessment of colonic polyp histopathology using probe-based confocal laser endomicroscopy.

Int J Colorectal Dis 2019 Dec 6;34(12):2043-2051. Epub 2019 Nov 6.

Department of Medicine, Section of Gastroenterology, VA Boston Healthcare System, Boston, MA, USA.

Introduction: Probe-based confocal laser endomicroscopy (pCLE) is a promising modality for classifying polyp histology in vivo, but decision making in real-time is hampered by high-magnification targeting and by the learning curve for image interpretation. The aim of this study is to test the feasibility of a system combining the use of a low-magnification, wider field-of-view pCLE probe and a computer-assisted diagnosis (CAD) algorithm that automatically classifies colonic polyps.

Methods: This feasibility study utilized images of polyps from 26 patients who underwent colonoscopy with pCLE. The pCLE images were reviewed offline by two expert and five junior endoscopists blinded to index histopathology. A subset of images was used to train classification software based on the consensus of two GI histopathologists. Images were processed to extract image features as inputs to a linear support vector machine classifier. We compared the CAD algorithm's prediction accuracy against the classification accuracy of the endoscopists.

Results: We utilized 96 neoplastic and 93 non-neoplastic confocal images from 27 neoplastic and 20 non-neoplastic polyps. The CAD algorithm had sensitivity of 95%, specificity of 94%, and accuracy of 94%. The expert endoscopists had sensitivities of 98% and 95%, specificities of 98% and 96%, and accuracies of 98% and 96%, while the junior endoscopists had, on average, a sensitivity of 60%, specificity of 85%, and accuracy of 73%.

Conclusion: The CAD algorithm showed comparable performance to offline review by expert endoscopists and improved performance when compared to junior endoscopists and may be useful for assisting clinical decision making in real time.
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http://dx.doi.org/10.1007/s00384-019-03406-yDOI Listing
December 2019

Spatial variability of arsenic in Indo-Gangetic basin of Varanasi and its cancer risk assessment.

Chemosphere 2020 Jan 19;238:124623. Epub 2019 Aug 19.

Division of Agricultural Physics, Indian Agricultural Research Institute, New Delhi, 110012, India.

The Indo-Gangetic alluvium is prime region for intensive agricultural. In some areas of this region, groundwater is now becoming progressively polluted by contamination with poisonous substances like arsenic. Intensive irrigation with arsenic contaminated ground water in dry spell results in the formation of As(III) which is more toxic. Thus groundwater quality assessment of Gangetic basin has become essential for its safer use. Therefore we under took study on the spatial variability of arsenic by collecting georeferred groundwater samples on grid basis from various water sources like dug well, bore and hand pumps covering the river bank region of Ganga basin. Water quality was investigated through determination pH, EC, TDS, salinity, Na, K, Ca, Mg, SAR, SSP, CO, HCO, RSC, Cl, As, Fe, Zn, Mn and Cu, etc. Results pointed severe As contamination in ground water of three sites of the study area. ARC GIS software is now able to process maps along with tabular data and compare them well, to provide the spatial visualization of information and using this tool, the Geographical Information System (GIS) of arsenic was developed. It was noticed from spatial maps that concentration of arsenic was more near the meandering points of Ganga.
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http://dx.doi.org/10.1016/j.chemosphere.2019.124623DOI Listing
January 2020

Method to Predict Glass Vial Fogging in Lyophilized Drug Products.

J Pharm Sci 2020 01 29;109(1):323-330. Epub 2019 Aug 29.

Lonza AG, Drug Product Services, Basel, Switzerland. Electronic address:

Glass fogging is a phenomenon occurring in lyophilized drug products and can be described as a thin product layer deposited on the inner surface of the glass container, in the area not covered by the lyo cake itself. It is often considered a cosmetic defect; however, the loss of container closure integrity is a potential consequence of the fogging's expansion to the vial neck region, making this a potential critical defect. Thus, a method for predicting the extent of vial fogging before the actual freeze-drying is of particular interest for the pharmaceutical industry. For that reason, we evaluated a simple method ("simulated fogging") applicable to drug product formulations in a specific container closure system. Two different vial types with different surface hydrophilicity were tested using 3 model protein formulations, comparing the simulated fogging test and the degree of fogging after actual lyophilization. The simulated fogging method could predict fogging and showed a correlation to fogging in lyophilized drug product glass vials. We observed that all formulations showed fogging in the hydrophilic vials. By contrast, hydrophobic vials prevented fogging, however, interestingly with remaining defects of so-called droplet formation. Other than extent of fogging, no additional differences of lyophilized cake properties or other product quality attributes were observed between products using the different glass vial types tested.
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http://dx.doi.org/10.1016/j.xphs.2019.08.024DOI Listing
January 2020

Microwave sensor for the investigation of glucose-dependent reflection properties in aqueous samples.

J Med Eng Technol 2019 May 29;43(4):217-222. Epub 2019 Aug 29.

Centre for Biomedical Engineering, Indian Institute of Technology , New Delhi , India.

The reported paper presents the development of a microwave sensor with a resonant frequency 2.4 GHz. The sensor is also demonstrated to investigate the variation in its response as a function of glucose concentration. The sensor could be used for the monitoring of blood glucose level in diabetics through non-invasive technology. The approach followed is based on the notion that, change in glucose concentration in the blood affects dielectric properties of blood which in turn produce an impact on reflection properties of the sensor. This effect on response of sensor will be ultimately used to estimate blood glucose concentration. The design specifications considered for the development of sensor are defined in the paper. The experimental setup for experiment and procedure employed for the investigation of the reflection properties of the sensor as a function of glucose concentration are also discussed in detail. The shift in resonance frequency and the change in the magnitude of the reflection coefficient of proposed sensor have been observed. The reported measurement results are the preliminary results in exploring the implementation of proposed sensor for non-invasive blood glucose monitoring.
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http://dx.doi.org/10.1080/03091902.2019.1653388DOI Listing
May 2019

Venous stasis-induced fibrinolysis prevents thrombosis in mice: role of α2-antiplasmin.

Blood 2019 09 8;134(12):970-978. Epub 2019 Aug 8.

Department of Medicine, The University of Arizona, College of Medicine, Phoenix, AZ; and.

Stasis of venous blood triggers deep vein thrombosis by activating coagulation, yet its effects on the fibrinolytic system are not fully understood. We examined the relationship between stasis, fibrinolysis, and the development of experimental venous thrombosis. Effects of stasis-induced deep vein thrombosis and fibrinolysis on thrombosis were examined by inferior vena cava ligation in congenic mice with and without α2-antiplasmin (α2AP), the primary inhibitor of plasmin. Venous thrombus weights were measured and thrombus composition was determined by Martius scarlet blue and immunofluorescence staining. Venous thrombi from α2AP mice contained plasminogen activators, plasminogen activator inhibitor-1, plasminogen, and α2AP, which changed with thrombus age. Normal, α2AP mice developed large, occlusive thrombi within 5 hours after ligation; thrombi were even larger in plasminogen-deficient mice ( < .001). No significant thrombus formation was seen in α2AP mice ( < .0001) or in α2AP mice treated with an α2AP-inactivating antibody ( < .001). Venous stasis activated fibrinolysis, measured by D-dimer levels, in α2AP mice vs α2AP mice ( < .05). Inhibition of fibrinolysis by the indirect plasmin inhibitor ε-aminocaproic acid or by α2AP restored thrombosis in α2AP mice. In addition to its effects on acute thrombosis, thrombus formation was also markedly suppressed in α2AP mice vs α2AP mice ( < .0001) 1, 7, and 14 days after ligation. We conclude that experimental venous stasis activates the fibrinolytic system to block the development of venous thrombosis. Suppression of fibrinolysis by α2AP appears essential for stasis-induced thrombus development, which suggests that targeting α2AP may prove useful for preventing venous thrombosis.
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http://dx.doi.org/10.1182/blood.2019000049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6753621PMC
September 2019

Variance Between Different Light Obscuration and Flow Imaging Microscopy Instruments and the Impact of Instrument Calibration.

J Pharm Sci 2019 07 4;108(7):2397-2405. Epub 2019 Mar 4.

Drug Product Services, Lonza, Basel, Switzerland. Electronic address:

Subvisible particles (SVPs) are an obligatory critical quality attribute of the product, and yet, they are found in all biopharmaceutical products intended for infusion or injection. Light obscuration (LO) is the primary pharmacopeial method used to quantify SVPs. However, the method may not be equally sensitive toward all particles that can possibly occur. Calibration of LO instruments is usually performed using polystyrene beads suspended in water. In this study, the dependence of the sizing accuracy of LO analysis was evaluated by using a calibration suspension of lower refractive index beads made of silica suspended in sucrose solution. It was demonstrated that the sizing accuracy was strongly dependent on the reference material's properties used for calibration. It was also demonstrated that flow imaging microscopy suffered from the same artifact, albeit to a smaller extent. We further tested different LO sensors and instruments. Interestingly, our results show that the sizing accuracy varied from instrument to instrument, strongly depending on the properties of the sensor. To summarize, sizing and counting accuracies were dependent on the material used for calibration and its optical properties as well as the calibration curve, the sensor, and the instrument supplier. Closer match of optical properties between calibration system and test system seems to improve the sensitivity of the measurement. The results of this study raise the following major practical implications: (1) LO and flow imaging microscopy are not truly orthogonal analytical methods, (2) while matching optimal properties of material used for calibration and test items increased sensitivity, this is of poor practical applicability given that analytes contain multiple particles, and (3) setting product-specific limits for SVPs require special considerations with regard to the data sets used.
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http://dx.doi.org/10.1016/j.xphs.2019.02.019DOI Listing
July 2019

Comparing Physical Container Closure Integrity Test Methods and Artificial Leak Methodologies.

PDA J Pharm Sci Technol 2019 May-Jun;73(3):220-234. Epub 2019 Jan 16.

Lonza Drug Product Services, Basel, Switzerland;

The sterility of drug products intended for parenteral administration is a critical quality attribute (CQA) because it serves to ensure patient safety and is thus a key requirement by health authorities. While sterility testing is a probabilistic test, the assurance of sterility is a holistic concept including adequate design of manufacturing facilities, process performance, and product design. Container closure integrity testing (CCIT) is necessary to confirm the integrity of a container closure system (CCS), until the end of a product's shelf life. The new and revised United States Pharmacopeia (USP) General Chapter <1207> is a comprehensive guidance on CCI. Nevertheless, practical considerations including the choice of CCIT methods, the acceptance criteria, or the positive control samples (artificial leaks) must be addressed by the pharmaceutical manufacturer.This study is the first to provide a systematic comparison of four commonly used physical CCIT (pCCIT) methods [Helium (He) leak, vacuum decay, laser-based headspace analysis (HSA), and dye ingress] and four commonly used modes of creating artificial leaks (laser-drilled micro holes, copper wire introduced leaks, and two types of capillary leaks).The results from these experiments provide comprehensive data to allow a direct comparison of the capabilities of the individual methods. The results confirmed that the He leak detection method, which is considered the "gold-standard" for pCCIT regarding method sensitivity, indeed demonstrates the highest detection sensitivity (lowest detection limit). In comparison to the dye ingress method, HSA and vacuum decay also demonstrated better detection sensitivity in our study.Capillary leaks with orifice diameter (capillary leak with flow according to an ideal orifice) and micro holes yielded similar leak rates, whereas capillaries with nominal diameters yielded significantly lower leak rates. In conclusion, method sensitivity cannot be compared by means of a leak diameter, but requires the consideration of multiple impacting factors (e.g., path length, uniformity). Sterility of drug products intended for parenteral administration is a critical quality attribute to ensure patient's safety and is thus a key requirement by health authorities. The absence of microbial contamination must be demonstrated by container closure integrity (CCI) of the container closure system (CCS). Currently, the revised United States Pharmacopeia (USP) General Chapter <1207> provides the most extensive guidance on how CCI should be assessed. Nevertheless, practical considerations on the choice of an appropriate CCIT method, artificial leaks or the choice of an acceptance criteria are lacking and must be addressed by the pharmaceutical manufacturer.This study provides a systematic comparison of four commonly used physical CCIT (pCCIT) methods [Helium (He) leak, vacuum decay, laser-based headspace analysis (HSA) and dye ingress] and four commonly used modes of creating artificial leaks (laser-drilled micro holes, copper wire introduced leaks, and two types of capillary leaks).
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http://dx.doi.org/10.5731/pdajpst.2018.009332DOI Listing
February 2020

In Silico Prediction of Diffusion Interaction Parameter (k), a Key Indicator of Antibody Solution Behaviors.

Pharm Res 2018 Aug 20;35(10):193. Epub 2018 Aug 20.

Biotherapeutics Pharmaceutical Sciences Research and Development, Pfizer Inc., 700 Chesterfield Parkway West, Chesterfield, Missouri, 63017, USA.

Purpose: To develop resource-sparing in silico approaches that aim to reduce experimental effort and material required by developability assessments (DA) of monoclonal antibody (mAb) drug candidates.

Methods: A battery of standardized biophysical experiments was performed on high concentration formulations of 16 drug product development stage mAbs using a platform buffer. Full-length molecular models of these mAbs were also generated via molecular modeling. These models were used to computationally estimate molecular descriptors of these 16 mAbs. Pairwise and multi-parameter correlations among experimentally measured biophysical attributes and calculated molecular descriptors were obtained via statistical analyses.

Results: Diffusion interaction parameter (k) showed statistically significant pairwise correlations (p-values <0.005) with thermal stability, viscosity, isoelectric point, and apparent solubility of the antibodies in our dataset. k also showed statistically significant pairwise correlations (p-values <0.005) with several computationally calculated molecular descriptors (pI, net charge, charge on the Fv region, and zeta potential.) These pairwise correlations were further refined by multivariate analyses. These analyses yielded several useful equations for prediction of k from antibody sequences, structural models, and experimentally measured biophysical attributes.

Conclusions: Diffusion interaction parameter (k) was found to be a key biophysical property for the mAbs in our dataset. It connects conformational heterogeneity of an antibody with its colloidal and rheological behaviors. The equations derived in this work shall enable rapid, resource-sparing, and cost-effective DAs of biologic drug candidates.
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http://dx.doi.org/10.1007/s11095-018-2466-6DOI Listing
August 2018

Are Injection Site Reactions in Monoclonal Antibody Therapies Caused by Polysorbate Excipient Degradants?

J Pharm Sci 2018 11 25;107(11):2735-2741. Epub 2018 Jul 25.

UnityPoint Cardiology, 1215 Pleasant, Suite 414, Des Moines, Iowa 50309.

Injection site reactions (ISRs) and other adverse side effects are commonly observed during therapy with biologics. These hypersensitivity-related side effects can vary from simple rash to life-threatening anaphylactic reaction and may be linked to the immunogenicity of the drug including formation of antidrug antibodies. Reactions can also occur as a consequence of excipients in the product. We report the case of a patient who developed erythematous ISRs to both commercial PCSK9i formulations and had to go off therapy even though efficacy was not impacted. Skin testing showed that the patient was reacting to the polysorbates. Polysorbates are added to stabilize the biotherapeutic. Polysorbates can also activate complement and lead to a range of acute hypersensitivity and systemic immunostimulation reactions. Oxidative degradation products can function as haptens by reacting with proteins at the injection site. Reactive degradation products may even form adducts with the biologic itself, creating a potential neoantigen. Further research is needed to understand the fundamental causes of ISRs. It is critical that only the highest quality raw material is used, and proper storage conditions are employed to minimize degradation of polysorbates in the product. Although complete elimination of ISRs is unlikely, all efforts must be made to minimize them.
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http://dx.doi.org/10.1016/j.xphs.2018.07.016DOI Listing
November 2018

Considerations for the Use of Polysorbates in Biopharmaceuticals.

Pharm Res 2018 May 24;35(8):148. Epub 2018 May 24.

Lonza, Basel, Switzerland.

Purpose: Polysorbates are commonly added to protein formulations and serve an important function as stabilizers. This paper reviews recent literature detailing some of the issues seen with the use of polysorbate 80 and polysorbate 20 in protein formulations. Based on this knowledge, a development strategy is proposed that leads to a control strategy for polysorbates in protein formulations.

Methods: A consortium of Biopharmaceutical scientists working in the area of protein formulations, shared experiences with polysorbates as stabilizers in their formulations.

Results: Based on the authors experiences and recent published literature, a recommendation is put forth for a development strategy which will lead into the appropriate control strategy for these excipients.

Conclusions: An appropriate control strategy may comprise one or more elements of raw material, in-process and manufacturing controls. Additionally, understanding the role, if any, polysorbates play during stability will require knowledge of the criticality of the excipient, based upon its impact on CQAs due to variations in concentration and degradation level.
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http://dx.doi.org/10.1007/s11095-018-2430-5DOI Listing
May 2018

Container Closure Integrity Testing of Prefilled Syringes.

J Pharm Sci 2018 08 5;107(8):2091-2097. Epub 2018 Apr 5.

Lonza AG, Drug Product Services, Basel, Switzerland. Electronic address:

Prefilled syringes (PFSs) are increasingly preferred over vials as container closure systems (CCSs) for injectable drug products when facilitated or self-administration is required. However, PFSs are more complex compared to CCSs consisting of vial, rubber stopper, and crimp cap. Container closure integrity (CCI) assurance and verification has been a specific challenge for PFSs as they feature several sealing areas. A comprehensive understanding of the CCS is necessary for an appropriate CCI assessment as well as for packaging development and qualification. A comprehensive CCI assessment of 6 different PFSs from 3 different manufacturers (including 1 polymeric PFS) was conducted using helium leak testing. PFS components were manipulated to systematically assess the contribution of the different sealing areas to CCI, namely rigid needle shield (RNS)/needle, RNS/tip cone, and the individual ribs of a syringe plunger. The polymeric PFS required an equilibrium measurement for accurate container closure integrity testing. The different sealing areas and a single plunger rib were shown to provide adequate CCI. Acceptable tip cap movement until the point of CCI failure was estimated. The assessment of acceptable tip cap movement demonstrated the importance of considering the RNS/tip cone seal design to ensure CCI of the PFS upon post assembly possesses and shipment.
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http://dx.doi.org/10.1016/j.xphs.2018.03.025DOI Listing
August 2018

Precision Medicine for CRC Patients in the Veteran Population: State-of-the-Art, Challenges and Research Directions.

Dig Dis Sci 2018 05 23;63(5):1123-1138. Epub 2018 Mar 23.

Washington DC VA Medical Center, Washington, DC, USA.

Colorectal cancer (CRC) accounts for ~9% of all cancers in the Veteran population, a fact which has focused a great deal of the attention of the VA's research and development efforts. A field-based meeting of CRC experts was convened to discuss both challenges and opportunities in precision medicine for CRC. This group, designated as the VA Colorectal Cancer Cell-genomics Consortium (VA4C), discussed advances in CRC biology, biomarkers, and imaging for early detection and prevention. There was also a discussion of precision treatment involving fluorescence-guided surgery, targeted chemotherapies and immunotherapies, and personalized cancer treatment approaches. The overarching goal was to identify modalities that might ultimately lead to personalized cancer diagnosis and treatment. This review summarizes the findings of this VA field-based meeting, in which much of the current knowledge on CRC prescreening and treatment was discussed. It was concluded that there is a need and an opportunity to identify new targets for both the prevention of CRC and the development of effective therapies for advanced disease. Also, developing methods integrating genomic testing with tumoroid-based clinical drug response might lead to more accurate diagnosis and prognostication and more effective personalized treatment of CRC.
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http://dx.doi.org/10.1007/s10620-018-5000-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5895694PMC
May 2018

Probing the Conformation of an IgG1 Monoclonal Antibody in Lyophilized Solids Using Solid-State Hydrogen-Deuterium Exchange with Mass Spectrometric Analysis (ssHDX-MS).

Mol Pharm 2018 02 22;15(2):356-368. Epub 2018 Jan 22.

Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University , West Lafayette, Indiana 47907, United States.

Therapeutic proteins are often formulated as lyophilized products to improve their stability and prolong shelf life. The stability of proteins in the solid-state has been correlated with preservation of native higher order structure and/or molecular mobility in the solid matrix, with varying success. In the studies reported here, we used solid-state hydrogen-deuterium exchange with mass spectrometric analysis (ssHDX-MS) to study the conformation of an IgG1 monoclonal antibody (mAb) in lyophilized solids and related the extent of ssHDX to aggregation during storage in the solid phase. The results demonstrate that the extent of ssHDX correlated better with aggregation rate during storage than did solid-state Fourier-transform infrared (ssFTIR) spectroscopic measurements. Interestingly, adding histidine to sucrose at different formulation pH conditions decreased aggregation of the mAb, an effect that did not correlate with structural or conformational changes as measured by ssFTIR or ssHDX-MS. Moreover, peptide-level ssHDX-MS analysis in four selected formulations demonstrated global changes across the structure of the mAb when lyophilized with sucrose, trehalose, or mannitol, whereas site-specific changes were observed when lyophilized with histidine as the sole excipient.
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http://dx.doi.org/10.1021/acs.molpharmaceut.7b00696DOI Listing
February 2018

Effects of Drying Process on an IgG1 Monoclonal Antibody Using Solid-State Hydrogen Deuterium Exchange with Mass Spectrometric Analysis (ssHDX-MS).

Pharm Res 2018 01 3;35(1):12. Epub 2018 Jan 3.

Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana, 47906, USA.

Purpose: Lyophilization and spray drying are widely used to manufacture solid forms of therapeutic proteins. Lyophilization is used to stabilize proteins vulnerable to degradation in solution, whereas spray drying is mainly used to prepare inhalation powders or as an alternative to freezing for storing bulk drug substance. Both processes impose stresses that may adversely affect protein structure, stability and bioactivity. Here, we compared lyophilization with and without controlled ice nucleation, and spray drying for their effects on the solid-state conformation and matrix interactions of a model IgG1 monoclonal antibody (mAb).

Methods: Solid-state conformation and matrix interactions of the mAb were probed using solid-state hydrogen-deuterium exchange with mass spectrometric analysis (ssHDX-MS), and solid-state Fourier transform infrared (ssFTIR) and solid-state fluorescence spectroscopies.

Results: mAb conformation and/or matrix interactions were most perturbed in mannitol-containing samples and the distribution of states was more heterogeneous in sucrose and trehalose samples that were spray dried.

Conclusions: The findings demonstrate the sensitivity of ssHDX-MS to changes weakly indicated by spectroscopic methods, and support the broader use of ssHDX-MS to probe formulation and process effects on proteins in solid samples.
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http://dx.doi.org/10.1007/s11095-017-2318-9DOI Listing
January 2018